plotTop10 {seq2pathway} | R Documentation

## A wrapper function to plot top10 test results.

### Description

Plot a vertical bar plot of odds ratios with red lines indicates -log10(fdr adjusted p-value) of the top10 results ordered by FDR. This plot is sorted by -log10(FDR) from large to small

### Usage

      plotTop10(res,fdr=0.05,or=2,myfileID=NULL)

### Arguments

`res` | A result table of FisherTest_GO_BP_MF_CC function, FisherTest_MsigDB function, single element of result list of gene2pathway_test function or any table with colnames : 'FDR', 'Fisher_odds', 'Intersect_gene'/'GeneSet'
`fdr` | A non-negative FDR cuttoff for the table 'res'. Default is 0.05.
`or` | A non-negative odds ratio cuttoff for the table 'res'. Default is 2.
`myfileID` | main title of the plot. Default is NULL.

### Author(s)

Xinan Holly Yang, Zhezhen Wang

### Examples

      data(dat_chip)
      data(GO_BP_list,package="seq2pathway.data")
      data(Des_BP_list,package="seq2pathway.data")
      newOntology <- list(GO_BP_list[1:200], Des_BP_list[1:200])
      FS_test<- FisherTest_GO_BP_MF_CC(gs=as.vector(rownames(dat_chip)),
                                     Ontology="newOntology", newOntology=newOntology)
      plotTop10(FS_test$newOntology)

[Package seq2pathway version 1.16.0 Index]